New: CloudBioLinux packages are now listed on biogems.info !

# biogem description by cite version released stars issues source build total 90d*) 7d   90d**)
downloads commits
bio
Bioinformatics library (...) !
BioRuby project
4 days
270
11
94648
5973
35
41
Parser of scientific names (...) !
Dmitry Mozzherin
4 weeks
19
3
52035
4666
0
22
Basic spreadsheet content extraction using apache poi (...)
Stuart Owen, Finn Bacall, Quyen Nguyen
6 weeks
6
2
43091
2207
0
1
Binder of samtools for Ruby, on the top (...) !
Ricardo Ramirez-Gonzalez, Dan MacLean, Raoul J.P. Bonnal
2 weeks
20
6
39780
3624
Biogem is a software generator for Ruby in (...) !
Raoul J.P. Bonnal, Pjotr Prins
13 months
14
11
39491
2122
Support for interacting with taverna 2 server (...) !
Robert Haines, Finn Bacall
4 months
2
...
30714
1705
Gadgets for bioinformatics (...)
Shintaro Katayama
2 years
1
26093
2382
The Ruby ucsc api: accessing the ucsc genome (...) !
Hiroyuki Mishima, Jan Aerts
15 months
14
1
25975
1591
0
0
Http requests to entrez e-utilities (...)
Jared Ning
10 weeks
4
...
24766
1349
0
3
Blast search made easy! (...) !
Anurag Priyam, Ben J Woodcroft, Vivek Rai et al.
6 weeks
24738
3839
A Ruby api for interacting with biomart services (...) !
Darren Oakley
3 years
18
5
23639
973
0
0
Support for interacting with taverna 2 workflows (...) !
Finn Bacall, Robert Haines, David Withers et al.
15 months
23433
1290
Create pretty svg-format images of features, gene models (...)
Dan MacLean
18 months
10
5
21663
2369
Gff3 parser for big data (...) !
Pjotr Prins
2 years
6
2
19333
977
0
0
Maf parser for BioRuby (...)
Clayton Wheeler
2 years
10
31
18747
1219
Interfaces with biomodel search engine (...) !
Niall Beard
3 years
1
...
16397
747
A biogem to submit jobs on a queue (...)
Francesco Strozzi
2 years
5
...
16328
1116
0
0
Very fast parallel blast xml to rdf/html/json/yaml/csv transformer (...) !
Pjotr Prins
8 weeks
12
1
15861
1632
Log4r wrapper with extra features for roles and (...) !
Pjotr Prins
3 years
4
2
15572
1024
0
0
A simple obo file handler (...) !
mjy
3 years
5
...
14307
614
0
0
An open source framework for transforming heterogeneous data (...)
Joachim Baran, Kevin B. Cohen, Geraint Duck et al.
6 months
12
3
11660
1307
A fast parser for fastq files (...)
Francesco Strozzi
3 years
10
...
11650
708
0
0
Swiss army knife of tabulated data; transforming/filtering tab/csv (...)
Pjotr Prins
13 months
9
20
11500
857
Support for multiple sequence alignments (msa) (...)
Pjotr Prins
13 months
8
5
11444
682
Data mining algorithms for jRuby (...)
arrigonialberto86
21 months
14
3
10327
1026
A tool to classify and manipulate pfemp1 dbl-alpha (...)
George Githinji
2 years
9802
566
Pipeline to remove contaminations from est libraries (...)
Philipp Comans
3 years
2
1
9630
469
0
0
Low memory sequence emitters (...)
Pjotr Prins
13 months
8
1
9375
567
Tool to work with polyploids, ngs and molecular (...)
Ricardo H.  Ramirez-Gonzalez
5 weeks
2
1
9322
2529
0
17
A nexus file format (phylogenetic inference) parser in (...) !
mjy
4 years
1
...
9078
342
Ruby support for the baclava file format (...) !
Robert Haines
16 months
1
...
8839
639
A wrapper for the signal peptide prediction algorith (...)
Ben J Woodcroft
11 months
3
...
8831
561
Build genome output files (...)
Michael Barton
23 months
5
...
8627
346
BioRuby assembly plugin (...) !
Chase Miller, Francesco Strozzi
4 years
4
...
8375
377
0
0
A BioRuby plugin for interaction with the transmembrane (...)
Ben J. Woodcroft
2 years
2
...
8199
467
0
0
Simple morphbank (http://morphbank.net) services accessor (...) !
mjy
3 years
1
...
8178
317
A biogem for counting small kmers for fingerprinting (...)
Ben J Woodcroft
2 years
5
...
8025
560
Lightweight Ruby api for ncbi eutils (...)
Joon Lee, aka seouri
2 years
8
...
7907
354
BioRuby plugin for reading and writing nexml (http://nexml.org) (...) !
Rutger Vos, Anurag Priyam
3 years
7
2
7884
376
Ruby wrapper for sambamba tool (...)
Artem Tarasov
2 years
2
...
7863
480
Supports linking of models within a ror application (...) !
Stuart Owen, Quyen Nguyen
2.2
15 months
...
7801
500
A BioRuby plugin for calculating the isoelectric point (...)
George Githinji, Pascal Betz
3 years
3
...
7727
410
This is a development release (...) !
Pjotr Prins and Trevor Wennblom
5 years
7595
255
Library for visualizing genomic regions (...) !
Jan Aerts
1.4
7 years
22
1
7102
287
0
0
A BioRuby plugin: handling genomic interavals and overlaps (...)
Hiroyuki Mishima
4 years
4
...
6993
289
0
0
Bio-ngs provides a framework for handling ngs data (...)
Francesco Strozzi, Raoul J.P. Bonnal
3 years
30
14
6739
274
0
0
Running and parsing of the protein transmembrane domain (...)
Ben J Woodcroft
4 years
1
...
6377
275
Reading/writing bgzf blocks (...)
Artem Tarasov, Clayton Wheeler
2 years
2
...
6174
400
Basespace Ruby sdk is a Ruby based software (...)
Joachim Baran, Raoul Bonnal, Eri Kibukawa et al.
23 months
13
2
5986
609
Ruby binding for bwa mapping software (...) !
Francesco Strozzi
4 years
4
...
5715
302
Gene ontology (go) interface for Ruby (...)
Ben J Woodcroft
4 years
10
...
5523
186
A plugin that allows you to parse large (...)
robsyme
4 years
1
...
5488
282
Taverna player is a rails plugin to run (...)
Robert Haines
4 months
4
3
5374
630
Read and manipulate cd-hit clusters (...)
George Githinji
2 years
5354
375
Iterate through a samtools pileup file (...)
Ben J. Woodcroft
2 years
2
...
5284
274
Ruby binding for samtools tabix (...)
throwern
21 months
3
...
5070
365
Api to ensembl databases (...) !
Jan Aerts, Francesco Strozzi
4 years
39
5
5021
169
Parser to work with file formats used in (...)
Ben J Woodcroft
5 months
...
4770
756
0
0
Fast multi-threaded vcf parser (...)
Pjotr Prins
6 months
20
4
4735
820
3
6
Ruby wrapper for the gff3-pltools (...)
Marjan Povolni
2 years
4465
276
Chembl rest api client, parser and container (...)
Mitsuteru Nakao
2 years
1
1
4415
285
0
0
Next-generation mapping of mutations (...)
Dan MacLean
2 years
2
...
4390
284
Ruby binding to the ucsc kent utilities (...)
throwern
2 years
2
...
4373
275
Geneexpression illuminahumanannotation (...)
Raoul J.P. Bonnal
4 years
1
...
4282
200
0
0
Implementation of the plasmoap algorithm (...)
Ben J Woodcroft
3 years
1
...
4251
201
Server for polymarker. to be used with cron (...)
Ricardo H.  Ramirez-Gonzalez
4 months
...
4075
891
Bioinformatics triple-store support (...)
Pjotr Prins
3 years
4
1
4021
195
Parse affymetrix cel/cdf files (...)
Pjotr Prins
3 years
2
1
3991
200
Timeseries modules for statsample (...)
Ankur Goel, Claudio Bustos
21 months
3844
365
BioRuby core plugins, most and stable plugins. blastxmlparser, (...) !
Raoul J.P. Bonnal
3 years
1
...
3706
178
BioRuby plugin for unichem rest web service (...)
Mitsuteru Nakao
2 years
3587
264
Programmatic interface to the cnls nuclear localisation signal (...)
Ben J. Woodcroft
3 years
2
...
3544
187
Rocker (...)
Luis (Coto) Orellana, Luis M. Rodriguez-R
4 weeks
3540
2653
Reports whether a nucleotide change results in synonymous (...)
Dan MacLean
2 years
...
3502
290
0
0
Enables the localisation predictor wolf psort to be (...)
Ben J Woodcroft
3 years
1
...
3493
189
0
0
This biogem is built around krona, a flashy (...)
Ben J. Woodcroft
22 months
1
...
3483
281
Parse pfam hmm definition files (...)
Ben J. Woodcroft
3 years
1
...
3164
192
A protparam compatible utility for BioRuby (...)
hryk
2 years
2
...
3096
191
Publish scientific results to the semantic web (...) !
Will Strinz
13 months
3
16
3083
475
0
0
Bio-gag is a biogem for detecting and correcting (...)
Ben J Woodcroft
2 years
2
...
3003
192
Ruby solution for ucsc liftover tool- (ucsc http://genome.ucsc.edu/cgi-bin/hgliftover) (...)
Andrei Rozanski
16 months
1
...
2702
366
0
0
Bindings to some internals of the velvet assembler (...)
Ben Woodcroft
5 months
1
2526
517
A general purpose framework for scripted handling of (...) development/stable
mjy
2 years
2
1
2450
762
BioRuby plugin for sun grid engine (...) !
Toshiaki Katayama
4 years
4
...
2210
102
Hello world plugin for the BioRuby (just for (...)
Toshiaki Katayama
4 years
3
...
2207
101
Digests dna based on restriction enzyme cut patterns (...) !
Trevor Wennblom
3 years
1
2204
101
0
0
Pass a full citation, get the bibtex back, (...) !
Matt Yoder
8 months
1
2187
505
0
0
Does high pairwise alignment of sequencing reads with (...)
John T. Prince
5 years
1
...
2107
81
Rubybhl is a simple request/response wrapper for the (...) !
Matt Yoder
17 months
6
...
2086
109
Gggenome Ruby client (...)
Mitsuteru Nakao
23 months
1
...
2012
185
Biostars data-mining and statistical analysis (...)
Joachim Baran
15 months
2002
286
A method to get the nucleotide sequence of (...)
Ben J Woodcroft
4 years
1
...
1949
103
Ruby ensembl rest api (...)
Alberto Donizetti
21 months
3
...
1934
188
BioRuby core ext: plugins which require external library (...) !
Raoul J.P. Bonnal, Pjotr Prins
3 years
1
...
1916
88
Restriction enzyme dataset (...) !
Sir Richard J. Roberts, Trevor Wennblom
3 years
...
1910
98
Meta package for biolinux distribution (...) !
Raoul J.P. Bonnal
3 years
2
...
1901
94
Generalized linear models for statsample (...)
Ankur Goel
21 months
1886
194
A Ruby api to the ensembl database (...) !
Jan Aerts, Francesco Strozzi
3 years
3
...
1882
96
Biological extensions for the intermine webservice client library (...) !
Alex Kalderimis
3 years
1
...
1875
410
One-line summary of your gem (...)
Toshiaki Katayama
3 years
1
...
1866
92
Decoding the dbsnp bitfield (...)
Hiroyuki Mishima
3 years
4
...
1857
98
Phyloxml plugin for BioRuby (...)
Diana Jaunzeikare, Clayton Wheeler
3 years
3
...
1839
106
Wrapper around the exportpred algorithm for predicting p (...)
Ben J Woodcroft
3 years
1
...
1824
97
0
0
A simple biogem that allows computation of the (...)
Ben J Woodcroft
3 years
1
...
1792
96
Hydropathy scale for BioRuby (...)
Ben J Woodcroft
3 years
1
...
1789
101
0
0
Enables parsing of hmmer version 3 reports (...)
Christian Zmasek, Ben J Woodcroft
3 years
1
1
1704
99
Dead simple method of running shell commands from (...)
Ben J. Woodcroft
17 months
...
1645
209
0
0
Interface for express beta diversity (...)
Ben J. Woodcroft
17 months
...
1616
187
Build graph with jRuby (...)
Matteo Picciolini
2 years
1601
102
A programmatic interface to the ipcress in-silico pcr (...)
Ben J Woodcroft
2 years
3
...
1592
104
Bio-repeatmasker (...)
Andrei Rozanski
18 months
1582
183
Client for xoopit's cloudquery api (...)
Cameron Walters, nb.io
6 years
5
...
1549
216
A parser for cigar format alignments (...)
Ben J Woodcroft
16 months
4
...
1480
212
Specimens quickly extracted and digitized, or just "squid" (...) alpha
Matt Yoder, Rich Flood
3 weeks
...
1403
1403
Reads metadata from integrated microbial genomes (img) metadata (...)
Ben J. Woodcroft
2 years
...
1345
96
0
0
Web server for bio-samtools (...)
homonecloco
13 months
...
1328
202
Parse stockholm sequence alignment format (...)
Ben J. Woodcroft
2 years
2
...
1143
108
0
0
Fast storage and comparison of chr+pos(+alt) locations (...)
Pjotr Prins
8 months
1111
188
Ruby wrapper to run standard-raxml for maximum likelihood (...)
Fernando Izquierdo
23 months
...
1069
99
0
0
Csshttprequest is cross-domain ajax using css as a (...)
Cameron Walters, Randy Reddig
6 years
90
1
1025
345
0
0
A sequence read archive (sra) download script and (...)
Ben J. Woodcroft
6 months
1
...
810
202
Helper methods for reading .delta files (...)
robsyme
3 months
...
783
347
Mine publications for gene names (...)
Pjotr Prins
16 months
...
739
98
0
0
A restful service for sharing genomic data (...) !
Joachim Baran, Robert Buels, Michel Dumontier
16 months
644
69
Ruby inferface for kseq.h by heng li for (...)
Fedor Gusev
11 months
1
...
599
107
A Ruby wrapper on the open tree api (...) beta
Matt Yoder
9 months
...
556
106
0
0
Tools to work with fasta files, indexed with (...)
homonecloco
9 months
...
515
107
Tools to manipulate blat files from the command (...)
homonecloco
9 months
...
497
96
Identifying problems with gene predictions (...) !
Monica Dragan, Ismail Moghul, Anurag Priyam et al.
5 weeks
474
474
Emulates as if old BioRuby biofetch alives (...)
Naohisa Goto
7 months
...
457
106
0
0
Faldo location output method for bio::location in BioRuby (...)
Joachim Baran, Naohisa Goto
7 months
...
457
108
(...) pre
pre
421
11
Csshttprequest is cross-domain ajax using css (...)
Cameron Walters, Randy Reddig
0.1
6 years
405
59
The api for freebayes version #{bio::freebayes::extversion} (...)
Natapol Pornputtapong
6 weeks
400
368
Aggregate fastqc (quality control for next generation sequencing (...)
Raoul Jean Pierre Bonnal
1 week
...
386
246
Api of picard tool (...)
Natapol Pornputtapong
6 weeks
317
193
A web app wrapper for genevalidator (...) !
Ismail Moghul
6 weeks
...
315
315
A pipeline manager (...)
Francesco Strozzi
3 months
10
10
263
135
(...) pre
pre
175
18
*) gem downloads (total & last 90 days) from rubygems.org as of 2015-07-05
**) number of commits on GitHub (last 7 days & last 90 days)